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Fix cellranger and bump version to 2.5.1 #288

Merged
merged 10 commits into from
Jan 22, 2024
Merged

Fix cellranger and bump version to 2.5.1 #288

merged 10 commits into from
Jan 22, 2024

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grst
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@grst grst commented Jan 18, 2024 •
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  • Somehow the cellranger module installed from modules was missing files, don't ask me how we ended up
    there
  • params.aligner was referenced incorrectly in scrnaseq.nf
  • Bump version to 2.5.1 to make a patch release

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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@grst grst changed the base branch from master to dev January 18, 2024 11:48
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github-actions bot commented Jan 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0a674f5

+| ✅ 161 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-22 07:25:06

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grst commented Jan 19, 2024

@nf-core-bot please fix linting

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grst commented Jan 19, 2024

@nf-core-bot fix linting

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grst commented Jan 19, 2024

Don't be nice to the bot -.-

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grst commented Jan 19, 2024

@nf-core-bot fix linting

@grst grst changed the title Update modules and fix missing variable error Fix cellranger and bump version to 2.5.1 Jan 22, 2024
@grst grst requested a review from fmalmeida January 22, 2024 10:18
fmalmeida
fmalmeida approved these changes Jan 22, 2024
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Looks good.
Most of the changes were automatically via nf-core update right?

.github/workflows/ci.yml
"test,docker --aligner alevin",
"test,docker --aligner kallisto",
"test,docker --aligner star",
"test,docker --aligner cellranger -stub",
"test,docker --aligner universc -stub",
"test,docker --aligner cellranger",
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What was the thing that was making it being - stub before?

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correct

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grst commented Jan 22, 2024

yes... the only two "real" changes are the params.aligner fix and the changes to ci.yml

@grst grst merged commit 737ef17 into dev Jan 22, 2024
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@grst grst deleted the module-update branch January 22, 2024 10:30
@vondoRishi
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I have run into error with test while running with test profile

nextflow run \
    nf-core/scrnaseq \
    --outdir test_out \
    -r 2.5.1 \
    -profile test

The error is

Command error:
.command.sh: line 2: samtools: command not found

Next, I have tried to test run with cellranger

nextflow run \
    nf-core/scrnaseq \
    --outdir test_out \
    --aligner cellranger \
    -r 2.5.1 \
    -profile test

This time the error is

Command error:
.command.sh: line 3: cellranger: command not found

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Hello hello,
You have also to select an execution profile.
Maybe,
-profile docker,test.

@vondoRishi
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Hello hello, You have also to select an execution profile. Maybe, -profile docker,test.

My silly mistake.
One more thing, the parameter --genome_fasta in the usage example is no longer exist. It should be only --fasta.
Thanks a lot.

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@fmalmeida fmalmeida fmalmeida approved these changes

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@grst @vondoRishi @fmalmeida @nf-core-bot